Amino Acid Degradation Pathways Research Articles

Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids.

Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. In all, 3,215 proteins were identified, over half of the open reading frames predicted from the genomic sequence. The abundance of 1,361 proteins displayed strong lifestyle bias. In total, 1,131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised approximately 12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis or gluconeogenesis, and the pentose phosphate pathway; however, several amino acid degradation pathways were repressed. This suggests that bacteroids maintain a relatively independent anabolic metabolism. Tricarboxylic acid cycle proteins were highly expressed in bacteroids and no other catabolic pathway emerged as an obvious candidate to supply energy and reductant to nitrogen fixation. Bacterial stress response proteins were induced in bacteroids. Many WSM419 proteins that are not encoded in S. meliloti Rm1021 were detected, and understanding the functions of these proteins might clarify why S. medicae WSM419 forms a more effective symbiosis with M. truncatula than S. meliloti Rm1021.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The diversity among the species Tetragenococcus halophilus including new isolates from a lupine seed fermentation

BackgroundTetragenococcus (T.) halophilus can be isolated from a variety of fermented foods, such as soy sauce, different soy pastes, salted fish sauce and from cheese brine or degraded sugar beet thick juice. This species contributes by the formation of short chain acids to the flavor of the product. Recently, T. halophilus has been identified as a dominant species in a seasoning sauce fermentation based on koji made with lupine seeds.ResultsIn this study we characterized six strains of T. halophilus isolated from lupine moromi fermentations in terms of their adaptation towards this fermentation environment, salt tolerance and production of biogenic amines. Phylogenic and genomic analysis revealed three distinctive lineages within the species T. halophilus with no relation to their isolation source, besides the lineage of T. halophilus subsp. flandriensis. All isolated strains from lupine moromi belong to one lineage in that any of the type strains are absent. The strains form lupine moromi could not convincingly be assigned to one of the current subspecies. Taken together with strain specific differences in the carbohydrate metabolism (arabinose, mannitol, melibiose, gluconate, galactonate) and amino acid degradation pathways such as arginine deiminase pathway (ADI) and the agmatine deiminase pathway (AgDI) the biodiversity in the species of T. halophilus is greater than expected. Among the new strains, some strains have a favorable combination of traits wanted in a starter culture.ConclusionsOur study characterized T. halophilus strains that were isolated from lupine fermentation. The lupine moromi environment appears to select strains with specific traits as all of the strains are phylogenetically closely related, which potentially can be used as a starter culture for lupine moromi. We also found that the strains can be clearly distinguished phylogenetically and phenotypically from the type strains of both subspecies T. halophilus subsp. halophilus and T. halophilus subsp. flandriensis.

Branched-Chain Amino Acids Catabolism Pathway Regulation Plays a Critical Role in the Improvement of Leukopenia Induced by Cyclophosphamide in 4T1 Tumor-Bearing Mice Treated With Lvjiaobuxue Granule.

Background: Cyclophosphamide is a common tumor chemotherapy drug used to treat various cancers. However, the resulting immunosuppression leads to leukopenia, which is a serious limiting factor in clinical application. Therefore, the introduction of immunomodulators as adjuvant therapy may help to reduce the hematological side effects of cyclophosphamide. Lvjiaobuxue granule has been widely used in the clinical treatment of gynecological diseases such as anemia and irregular menstruation. Recently, it has been found to increase the function of white blood cells, but its mechanism of action is still unclear. We aimed to reveal the mechanisms of Lvjiaobuxue granule against acute leukopenia by an integrated strategy combining metabolomics with network pharmacology. Methods: Subcutaneously inoculated 4T1 breast cancer cells to prepare tumor-bearing mice, intraperitoneal injection of cyclophosphamide to establish a 4T1 tumor-bearing mice leukopenia animal model, using pharmacodynamic indicators, metabolomics, network pharmacology and molecular biology and other technical methods. To comprehensively and systematically elucidate the effect and mechanism of Lvjiaobuxue granule in improving cyclophosphamide-induced leukopenia in 4T1 tumor-bearing mice. Results: Lvjiaobuxue granule can improve the blood routine parameters and organ index levels of the leukopenia model of 4T1 tumor-bearing mice. Metabolomics studies revealed that 15 endogenous metabolites in the spleen of mice were considered as potential biomarkers of Lvjiaobuxue granule for their protective effect. Metabonomics and network pharmacology integrated analysis indicated that Lvjiaobuxue granule exerted the leukocyte elevation activity by inhibiting the branched-chain amino acids (BCAAs) degradation pathway and increasing the levels of valine, leucine and isoleucine. The results of molecular biology also showed that Lvjiaobuxue granule can significantly regulate the key enzymes in the catabolism of BCAAs, which further illustrates the importance of BCAAs in improving leukopenia. Conclusion: Lvjiaobuxue granule exerts obvious pharmacological effects on the leukopenia model of 4T1 tumor-bearing mice induced by cyclophosphamide, which could be mediated by regulating the branched-chain amino acid degradation pathway and the levels of valine, leucine and isoleucine.

Transcriptomic and isotopic data reveal central role of ammonium in facilitating the growth of the mixotrophic dinoflagellate, Dinophysis acuminata

Dinophysis spp. are mixotrophs that are dependent on specific prey, but are also potentially reliant on dissolved nutrients. The extent to which Dinophysis relies on exogenous N and the specific biochemical pathways important for supporting its autotrophic and heterotrophic growth are unknown. Here, the nutritional ecology of Dinophysis was explored using two approaches: 1) 15N tracer experiments were conducted to quantify the concentration-dependent uptake rates and associated kinetics of various N compounds (nitrate, ammonium, urea) of Dinophysis cultures and 2) the transcriptomic responses of Dinophysis cultures grown with multiple combinations of prey and nutrients were assessed via dinoflagellate spliced leader-based transcriptome profiling. Of the N compounds examined, ammonium had the highest Vmax and affinity coefficient, and lowest Ks for both pre-starved and pre-fed cultures, collectively demonstrating the preference of Dinophysis for this N source while little-to-no nitrate uptake was observed. During the transcriptome experiments, Dinophysis grown with nitrate and without prey had the largest number of genes with lower transcript abundances, did not increase abundance of transcripts associated with nitrate/nitrite uptake or reduction, and displayed no cellular growth, suggesting D. acuminata is not capable of growing on nitrate. When offered prey, the transcriptomic response of Dinophysis included the production of phagolysosomes, enzymes involved in protein and lipid catabolism, and N acquisition through amino acid degradation pathways. Compared with cultures only offered ammonium or prey, cultures offered both ammonium and prey had the largest number of genes with increased transcript abundances, the highest growth rate, and the unique activation of multiple pathways involved in cellular catabolism, further evidencing the ability of Dinophysis to grow optimally as a mixotroph. Collectively, this study evidences the key role ammonium plays in the mixotrophic growth of Dinophysis and reveals the precise biochemical pathways that facilitate its mixotrophic growth.

Network analysis of the effects of long non-coding RNAs in artemisinin treatment of atherosclerosis in APOE-/- mice.

Atherosclerosis has become a worldwide medical burden. Our previous studies have shown that artemisinin (ART) had the capability to reduce atherosclerosis. Emerging evidence indicates that long non-coding RNAs (lncRNAs) are involved in the development of atherosclerosis. However, whether lncRNAs might participate in the mechanism through which artemisinin mitigates atherosclerosis has not been reported. Eight-week-old apolipoprotein E deficient (APOE-/-) mice were divided into two groups, one of which was treated with artemisinin. Red oil O staining was used to measure the sizes of the atherosclerotic lesions. We conducted deep sequencing to investigate lncRNA profiles in the aorta tissue in high-fat diet fed APOE knockdown mice with and without artemisinin treatment. CeRNA network, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were performed through bioinformatics analysis. RT-PCR was used to validate the differentially expressed lncRNAs. A total of 102 lncRNAs and 4,630 mRNAs were differentially expressed (p < 0.05) between the artemisinin treatment group and atherosclerosis model group. KEGG and GO analyses indicated that the categories metabolic process, specific amino acid degradation and PI3K-Akt signaling pathway are involved in the effects of artemisinin treatment in atherosclerosis (q < 0.05). LncRNA ENSMUST00000099676.4, ENSMUST00000143673.1, ENSMUST00000070085.5 and ENSMUST00000224554 might be engaged in the treatment mechanism through which artemisinin alleviates atherosclerosis. These findings indicated the possible mechanism and therapeutic role of lncRNAs in artemisinin treatment of atherosclerosis and provided a theoretical basis for the future application of artemisinin in patients with atherosclerosis.

Multiomics-Identified Intervention to Restore Ethanol-Induced Dysregulated Proteostasis and Secondary Sarcopenia in Alcoholic Liver Disease.

Signaling and metabolic perturbations contribute to dysregulated skeletal muscle protein homeostasis and secondary sarcopenia in response to a number of cellular stressors including ethanol exposure. Using an innovative multiomics-based curating of unbiased data, we identified molecular and metabolic therapeutic targets and experimentally validated restoration of protein homeostasis in an ethanol-fed mouse model of liver disease. Studies were performed in ethanol-treated differentiated C2C12 myotubes and physiological relevance established in an ethanol-fed mouse model of alcohol-related liver disease (mALD) or pair-fed control C57BL/6 mice. Transcriptome and proteome from ethanol treated-myotubes and gastrocnemius muscle from mALD and pair-fed mice were analyzed to identify target pathways and molecules. Readouts including signaling responses and autophagy markers by immunoblots, mitochondrial oxidative function and free radical generation, and metabolic studies by gas chromatography-mass spectrometry and sarcopenic phenotype by imaging. Multiomics analyses showed that ethanol impaired skeletal muscle mTORC1 signaling, mitochondrial oxidative pathways, including intermediary metabolite regulatory genes, interleukin-6, and amino acid degradation pathways are β-hydroxymethyl-butyrate targets. Ethanol decreased mTORC1 signaling, increased autophagy flux, impaired mitochondrial oxidative function with decreased tricarboxylic acid cycle intermediary metabolites, ATP synthesis, protein synthesis and myotube diameter that were reversed by HMB. Consistently, skeletal muscle from mALD had decreased mTORC1 signaling, reduced fractional and total muscle protein synthesis rates, increased autophagy markers, lower intermediary metabolite concentrations, and lower muscle mass and fiber diameter that were reversed by β-hydroxymethyl-butyrate treatment. An innovative multiomics approach followed by experimental validation showed that β-hydroxymethyl-butyrate restores muscle protein homeostasis in liver disease.

Abstract 13921: Targeting Receptor-Interacting Protein 140 to Modulate Energy Metabolism in the Failing Heart

The nuclear receptors, peroxisome proliferator-activated receptors (PPARs), estrogen-related receptors (ERRs), and their co-regulator PPARγ coactivator-1α (PGC-1α), control postnatal cardiac mitochondrial biogenesis and energy metabolism. During the development of heart failure (HF), the activity of PGC-1/PPAR/ERR is reduced resulting in diminished capacity for fatty acid oxidation (FAO) and ATP production potentially contributing to an “energy-starved” state that contributes to progression of HF. Receptor-Interacting protein 140 (RIP140) serves as a co-repressor of PGC-1/PPAR/ERR in skeletal muscle and adipose tissue. We hypothesized that RIP140 represses cardiac energy metabolism in the normal and failing heart. Accordingly, we targeted Nrip1 (encoding RIP140) using a muscle creatinine kinase (MCK)-driven Cre recombinase to generate striated muscle-specific RIP140 knockout (msRIP140 KO) mice. msRIP140 KO mice appeared normal at baseline with no difference in survival or cardiac systolic function compared to littermate controls. RNA-sequence analysis demonstrated that the expression of genes involved in a wide array of mitochondrial energy metabolic pathways including FAO, tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), and branched-chain amino acid (BCAA) degradation pathways were upregulated in msRIP140 KO ventricles, and in msRIP140 KO skeletal muscle. msRIP140 KO mice exhibited significantly less cardiac hypertrophy and diastolic dysfunction in response to chronic pressure overload. Next, cardiac-specific (cs) RIP140 KO mice were generated and subjected to transverse aortic constriction/apical myocardial infarction surgery (TAC/MI), an established HF model. csRIP140 KO mice exhibited less cardiac remodeling and systolic dysfunction compared to littermate controls, along with less downregulation of metabolic genes and induction of cardiac stress ( Nppa and Nppb ) and fibrosis response markers ( Tgfb2 and Col3a1 ). We conclude that RIP140 serves as a global co-repressor of cardiac energy metabolic genes in the adult heart and that modulation of RIP140 activity could prove to be a novel therapeutic approach for HF.

Low-temperature effects on docosahexaenoic acid biosynthesis in Schizochytrium sp. TIO01 and its proposed underlying mechanism

BackgroundSchizochytrium species are known for their abundant production of docosahexaenoic acid (DHA). Low temperatures can promote the biosynthesis of polyunsaturated fatty acids (PUFAs) in many species. This study investigates low-temperature effects on DHA biosynthesis in Schizochytrium sp. TIO01 and its underlying mechanism.ResultsThe Schizochytrium fatty acid biosynthesis pathway was evaluated based on de novo genome assembly (contig N50 = 2.86 Mb) and iTRAQ-based protein identification. Our findings revealed that desaturases, involved in DHA synthesis via the fatty acid synthase (FAS) pathway, were completely absent. The polyketide synthase (PKS) pathway and the FAS pathway are, respectively, responsible for DHA and saturated fatty acid synthesis in Schizochytrium. Analysis of fatty acid composition profiles indicates that low temperature has a significant impact on the production of DHA in Schizochytrium, increasing the DHA content from 43 to 65% of total fatty acids. However, the expression levels of PKS pathway genes were not significantly regulated as the DHA content increased. Further, gene expression analysis showed that pathways related to the production of substrates (acetyl-CoA and NADPH) for fatty acid synthesis (the branched-chain amino acid degradation pathway and the pentose phosphate pathway) and genes related to saturated fatty acid biosynthesis (the FAS pathway genes and malic enzyme) were, respectively, upregulated and downregulated. These results indicate that low temperatures increase the DHA content by likely promoting the entry of relatively large amounts of substrates into the PKS pathway.ConclusionsIn this study, we provide genomic, proteomic, and transcriptomic evidence for the fatty acid synthesis pathway in Schizochytrium and propose a mechanism by which low temperatures promote the accumulation of DHA in Schizochytrium. The high-quality and nearly complete genome sequence of Schizochytrium provides a valuable reference for investigating the regulation of polyunsaturated fatty acid biosynthesis and the evolutionary characteristics of Thraustochytriidae species.

Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis.

SummaryCOVID-19 (coronavirus disease 2019) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although the pathophysiology of this virus is complex and largely unknown, we employed a network-biology-fueled approach and integrated transcriptome data pertaining to lung epithelial cells with human interactome to generate Calu-3-specific human-SARS-CoV-2 interactome (CSI). Topological clustering and pathway enrichment analysis show that SARS-CoV-2 targets central nodes of the host-viral network, which participate in core functional pathways. Network centrality analyses discover 33 high-value SARS-CoV-2 targets, which are possibly involved in viral entry, proliferation, and survival to establish infection and facilitate disease progression. Our probabilistic modeling framework elucidates critical regulatory circuitry and molecular events pertinent to COVID-19, particularly the host-modifying responses and cytokine storm. Overall, our network-centric analyses reveal novel molecular components, uncover structural and functional modules, and provide molecular insights into the pathogenicity of SARS-CoV-2 that may help foster effective therapeutic design.

Effect of glycerol feed-supplementation on seabass metabolism and gut microbiota

Dietary glycerol supplementation in aquaculture feed is seen as an alternative and inexpensive way to fuel fish metabolism, attenuate metabolic utilization of dietary proteins and, subsequently, reduce nitrogen excretion. In this study, we evaluated the impact of dietary glycerol supplementation on nitrogen excretion of European seabass (Dicentrarchus labrax) and its effects on metabolite profile and bacterial community composition of gut digesta. These effects were evaluated in a 60-day trial with fish fed diets supplemented with 2.5% or 5% (w/w) refined glycerol and without glycerol supplementation. Nuclear magnetic resonance spectroscopy and high-throughput 16S rRNA gene sequencing were used to characterize the effects of glycerol supplementation on digesta metabolite and bacterial community composition of 6-h postprandial fish. Our results showed that ammonia excretion was not altered by dietary glycerol supplementation, and the highest glycerol dosage was associated with significant increases in amino acids and a decrease of ergogenic creatine in digesta metabolome. Concomitantly, significant decreases in putative amino acid degradation pathways were detected in the predicted metagenome analysis, suggesting a metabolic shift. Taxon-specific analysis revealed significant increases in abundance of some specific genera (e.g., Burkholderia and Vibrio) and bacterial diversity. Overall, our results indicate glycerol supplementation may decrease amino acid catabolism without adversely affecting fish gut bacterial communities.Key points• Glycerol can be an inexpensive and energetic alternative in fish feed formulations.• Glycerol did not affect nitrogen excretion and gut bacteriome composition.• Glycerol reduced uptake of amino acids and increased uptake of ergogenic creatine.• Glycerol reduced putative amino acid degradation pathways in predicted metagenome.

Effects of hydraulic retention time on the process performance and microbial community structure of an anaerobic single-stage semi-pilot scale reactor for the treatment of food waste

The performance of a single-stage semi-pilot scale reactor in anaerobically digesting food waste was examined and its microbial community composition investigated using high-throughput 16S rRNA gene sequencing. Highest biogas yield (1.01 L/g VSadded), highest removal efficiency for chemical oxygen demand (COD) (95.84%) and volatile solid (VS) (92.7%) were achieved during 124-day HRT. When the hydraulic retention time (HRT) reduced from 124 days to 62 days, ammonia and volatile fatty acids (VFA) concentration in the reactor gradually increased while pH, biogas yield, removal efficiency for VS and COD decreased gradually. This was likely due to the accumulation of volatile fatty acid (VFA), which resulted in scum accumulating in the reactor. The abundance of acid-producing bacteria resulted in the accumulation of VFA in the reactor, which is a critical factor that could explain process failure. Hydrogenotrophic methanogenesis was the main pathway for producing methane from hydrogen and carbon dioxide during the 124-day HRT. The decline in hydrogenotrophic methanogens at 62-day HRT inhibited the decomposition of VFA and accelerated the transfer of the amino acid degradation pathway, which further enhanced VFA accumulation. However, the dominant methanogens failed to degrade the excessive acetate at 41-day HRT. This metabolic discrepancy ultimately led to process deterioration.

Transcriptomic Characterization of Inhalation Phosphine‐Induced Cardiotoxicity in the Pediatric Rat

Phosphine (PH3) is a highly toxic, colorless, and odorless gas commonly used as a pesticide and rodenticide in the agricultural industry. PH3 is generated from metal phosphide tablets that can be purchased in both over‐the‐counter and restricted commercial‐use formulations. Due to phosphine’s widespread use, human exposures are common. Across documented cases of PH3 exposure, children show higher morbidity and mortality than adults. In pediatric case reports, exposure often results in impaired cardiac output and cardiac arrest. PH3 has a poorly defined mechanism of toxicity, but is suspected to bind iron centers of proteins in the electron transport chain and disrupt mitochondrial function. The pathways by which PH3 toxicity develops are unknown, and previous studies have focused exclusively on adult models. In order to characterize the toxic mechanisms of PH3 exposure in children, a pediatric rodent model of inhalation phosphine exposure was developed. Male and female Sprague Dawley rats at post‐natal day (PND) ages 21, 28, and 42 were exposed to PH3 via nose‐only inhalation. Female rats at PND 28 were found to have the lowest median lethal concentration x time (LCt50). Female PND 28 rats were used for transcriptomic analysis to identify toxic pathways associated with PH3 inhalation. Rats were exposed to either air or the LCt50 of PH3 (14,119 ppm x min) for 20 minutes and removed from the nose‐only inhalation system after an additional 5‐minute “off gas” period. Cardiac tissue was collected at 0.5, 1, 3, 6, and 24 hours post‐exposure and immediately snap frozen in liquid nitrogen. Total RNA was extracted and processed for microarray. Differences in gene expression between exposure groups were identified using Partek Genomics Suite, and identified genes were mapped to relevant pathways using Ingenuity Pathway Analysis (IPA) software. Microarray analysis revealed a biphasic gene expression pattern with the most changes occurring at 3 and 24 hours after phosphine exposure. At 3 hours post‐exposure, the changes in gene expression mapped to pathways involved with cellular function and maintenance and cardiac enlargement. In addition, upstream analysis suggested a role for norepinephrine in phosphine‐induced cardiotoxicity. At 24 hours post‐exposure, activation of the sirtuin signaling pathway, modulation of the mitochondrial permeability transition pore, and altered expression of mitochondrial membrane translocases TOMM7, TOMM22, and TOMM40 were observed. In addition, gene expression changes associated with metabolic reprogramming were detected. Branched chain amino acid degradation and fatty acid beta oxidation pathways were predicted to be inhibited, with downregulation of electron transport chain complexes I and V. These data support PH3 as a metabolic poison. Future analyses of these data will be used to identify additional pathways associated with phosphine toxicity.Support or Funding InformationThe research described was supported by an interagency agreement (AOD18014‐001‐00000) between the NIH Office of the Director (OD) and the USAMRICD under the oversight of the Chemical Countermeasures Research Program at the National Institute of Allergy and Infectious Diseases.

Understanding acute metabolic decompensation in propionic and methylmalonic acidemias: a deep metabolic phenotyping approach

BackgroundPathophysiology of life-threatening acute metabolic decompensations (AMD) in propionic acidemia (PA) and isolated methylmalonic acidemia (MMA) is insufficiently understood. Here, we study the metabolomes of PA and MMA patients over time, to improve insight in which biochemical processes are at play during AMD.MethodsLongitudinal data from clinical chemistry analyses and metabolic assays over the life-course of 11 PA and 13 MMA patients were studied retrospectively. Direct-infusion high-resolution mass spectrometry was performed on 234 and 154 remnant dried blood spot and plasma samples of PA and MMA patients, respectively. In addition, a systematic literature search was performed on reported biomarkers. All results were integrated in an assessment of biochemical processes at play during AMD.ResultsWe confirmed many of the metabolite alterations reported in literature, including increases of plasma valine and isoleucine during AMD in PA patients. We revealed that plasma leucine and phenylalanine, and urinary pyruvic acid were increased during AMD in PA patients. 3-hydroxyisovaleric acid correlated positively with plasma ammonia. We found that known diagnostic biomarkers were not significantly further increased, while intermediates of the branched-chain amino acid (BCAA) degradation pathway were significantly increased during AMD.ConclusionsWe revealed that during AMD in PA and MMA, BCAA and BCAA intermediates accumulate, while known diagnostic biomarkers remain essentially unaltered. This implies that these acidic BCAA intermediates are responsible for metabolic acidosis. Based on this, we suggest to measure plasma 3-hydroxyisovaleric acid and urinary ketones or 3-hydroxybutyric acid for the biochemical follow-up of a patient’s metabolic stability.

Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus

Microbial coculture to mimic the ecological habitat has been suggested as an approach to elucidate the effect of microbial interaction on secondary metabolite biosynthesis of Streptomyces. However, because of chemical complexity during coculture, underlying mechanisms are largely unknown. Here, we found that iron competition triggered antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus. During coculture, M. xanthus enhanced the production of a siderophore, myxochelin, leading M. xanthus to dominate iron scavenging and S. coelicolor to experience iron-restricted conditions. This chemical competition, but not physical contact, activated the actinorhodin biosynthetic gene cluster and the branched-chain amino acid degradation pathway which imply the potential to produce precursors, along with activation of a novel actinorhodin export system. Furthermore, we found that iron restriction increased the expression of 21 secondary metabolite biosynthetic gene clusters (smBGCs) in other Streptomyces species. These findings suggested that the availability for key ions stimulates specific smBGCs, which had the potential to enhance secondary metabolite biosynthesis in Streptomyces.

Microcystin-LR Degradation and Gene Regulation of Microcystin-Degrading Novosphingobium sp. THN1 at Different Carbon Concentrations.

The bacterium Novosphingobium sp. THN1 (THN1) is capable of degrading microcystin-LR (MC-LR). To study the ability of THN1 to degrade MC-LR and its possible mechanism(s) of regulation, we analyzed the effect of carbon concentrations on the degradation process. The MC-LR degradation rate peaked early and then declined during MC-LR biodegradation. Decreased levels of carbon in the medium caused the degradation peak to occur earlier. The expression of the functional gene mlrA, encoding a microcystinase, showed a similar trend to the MC-LR degradation rate at various carbon concentrations (r2 = 0.717, p < 0.05), suggesting that regulation of mlrA expression may play an important role in MC-LR degradation by THN1. The total bacterial biomass decreased when the carbon source was limited and did not correlate with the MC-LR degradation rate. Transcriptomic analysis showed that MC-LR degradation differentially regulated 62.16% (2597/4178) of THN1 genes. A considerable number of differentially expressed genes (DEGs) during MC-LR degradation encoded proteins related to carbon-, nitrogen-, and amino acid-related pathways. At 2 h of MC-LR degradation, most DEGs (29/33) involved in carbon and nitrogen metabolism were downregulated. This indicated that MC-LR may regulate carbon and nitrogen pathways of Novosphingobium sp. THN1. KEGG pathway analysis indicated that the upregulated DEGs during MC-LR degradation were mainly related to amino acid degradation and substrate metabolism pathways. Particularly, we detected increased expression of glutathione metabolism-related genes from transcriptomic data at 2 h of MC-LR degradation compared with the gene expression of 0 h, such as GST family protein, glutathione peroxidase, S-(hydroxymethyl) glutathione dehydrogenase, and glutathione-dependent disulfide-bond oxidoreductase that have been reported to be involved in microcystin degradation.

AMP-activated protein kinase signaling regulated expression of urea cycle enzymes in response to changes in dietary protein intake.

Abundance of urea cycle enzymes in the liver is regulated by dietary protein intake. Although urea cycle enzyme levels rise in response to a high-protein (HP) diet, signaling networks that sense dietary protein intake and trigger changes in expression of urea cycle genes have not been identified. The aim of this study was to identify signaling pathway(s) that respond to changes in protein intake and regulate expression of urea cycle genes in mice and human hepatocytes. Mice were adapted to either HP or low-protein diets followed by isolation of liver protein and mRNA and integrated analysis of the proteomic and transcriptomic data. HP diet led to increased expression of mRNA and enzymes in amino acid degradation pathways and decreased expression of mRNA and enzymes in carbohydrate and fat metabolism, which implicated adenosine monophosphate-activated protein kinase (AMPK) as a possible regulator. Primary human hepatocytes, treated with 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) an activator of AMPK, were used to test whether AMPK regulates expression of urea cycle genes. The abundance of carbamoylphosphate synthetase 1 and ornithine transcarbamylase mRNA increased in hepatocytes treated with AICAR, which supports a role for AMPK signaling in regulation of the urea cycle. Because AMPK is either a target of drugs used to treat type-2 diabetes, these drugs might increase the expression of urea cycle enzymes in patients with partial urea cycle disorders, which could be the basis of a new therapeutic approach.

Formation of phenylacetic acid and benzaldehyde by degradation of phenylalanine in the presence of lipid hydroperoxides: New routes in the amino acid degradation pathways initiated by lipid oxidation products

Lipid oxidation is a main source of reactive carbonyls, and these compounds have been shown both to degrade amino acids by carbonyl-amine reactions and to produce important food flavors. However, reactive carbonyls are not the only products of the lipid oxidation pathway. Lipid oxidation also produces free radicals. Nevertheless, the contribution of these lipid radicals to the production of food flavors by degradation of amino acid derivatives is mostly unknown. In an attempt to investigate new routes of flavor formation, this study describes the degradation of phenylalanine, phenylpyruvic acid, phenylacetaldehyde, and β-phenylethylamine in the presence of the 13-hydroperoxide of linoleic acid, 4-oxononenal (a reactive carbonyl derived from this hydroperoxide), and the mixture of both of them. The obtained results show the formation of phenylacetic acid and benzaldehyde in these reactions as a consequence of the combined action of carbonyl-amine and free radical reactions for amino acid degradation.

Understanding lipogenesis by dynamically profiling transcriptional activity of lipogenic promoters in Yarrowia lipolytica.

Lipogenesis is a complicated process involving global transcriptional reprogramming of lipogenic pathways. It is commonly believed that nitrogen starvation triggers a metabolic shift that reroutes carbon flux from Krebs cycles to lipogenesis. In this study, we systematically surveyed and dynamically profiled the transcriptional activity of 22 lipogenic promoters aiming to delineate a picture how nitrogen starvation regulates lipogenesis in Y. lipolytica. These lipogenic promoters drive the expression of critical pathways that are responsible for the generation of reducing equivalents (NADPH), carbon backbones (acetyl-CoA, malonyl-CoA, DHAP, etc.), synthesis and degradation of fatty acids. Specifically, our investigated promoters span across an array of metabolic pathways, including glycolysis, Krebs cycle, pentose phosphate pathway, mannitol cycle, glutamine-GABA cycle, fatty acid and lipid synthesis, glyoxylate, β-oxidation, and POM (pyruvate-oxaloacetate-malate) cycle. Our work provides evidences that mannitol cycle, glutamine-GABA cycle and amino acid degradation, pyruvate oxidation, and acetate assimilation pathways are lipogenesis-related steps involved in generating cytosolic NADPH and acetyl-CoA precursors. This systematic investigation and dynamic profiling of lipogenic promoters may help us better understand lipogenesis, facilitate the formulation of structure-based kinetic models, as well as develop efficient cell factories for fuels and chemical production in oleaginous species.

Another bottleneck for nitrogen mineralization in temperate forest soils: Arginine metabolism in microorganisms

Soil nitrogen (N) mineralization is generally limited by microbial N assimilation when microorganisms are exposed to substrates with high carbon-to-nitrogen (C/N) ratios. We hypothesized that microbial N release is also limited by repression of arginine-degrading activity in forest soils with the high C/N ratios. We analyzed the microbial assimilation and mineralization rates of 14C-labeled amino acid mixture, arginine, ornithine, and urea added to a variety of forest and cropland soils. The proportions of amino acid mixture derived 14C incorporated into microbial biomass (MB14C) in a 24-h incubation (3.7–20.4%) increased with soil C/N ratio and an increase in MB14C retards inorganic N release in the forest soils. Arginine mineralization displays a contrary pattern to amino acid derived MB14C and decreased with increasing soil C/N ratio. The reduced arginine-degrading activity in the forest soils with the high C/N ratios is consistent with general microbial N assimilation associated with growth, but it also correlates with the enhanced fungi-specific N preservation (e.g., recycling of ammonium in urea-ornithine cycle and accumulation of arginine or ornithine in vacuoles). Arginine or ornithine degradation is one of slower amino acid degradation pathways and potentially retards N mineralization in N-limited forest soils.

Genetically-Regulated Mechanisms of Insulin Resistance in Adipose Tissue

Insulin resistance (IR) is a harbinger of type 2 diabetes (T2D) and partly determined by genetic factors. However, genetically-regulated mechanisms of IR remain poorly understood. Using gene expression, genotype, and insulin sensitivity (SI and Matsuda index from FSIVGT and OGTT) data from an African American cohort (AAGMEx, N=256), we performed transcript-wide association and expression quantitative trait loci (eQTL) analyses to identify IR-associated cis-regulated transcripts (cis-eGenes) in adipose tissue. Data from a European ancestry cohort (METSIM, N=770) was used for testing replication of Matsuda index-associated cis-eGenes. In vitro genetic silencing studies were performed in a human adipocyte model to define the molecular mechanism of selected genes. Expression level of 2724 transcripts in adipose were negatively (1338) or positively (1386) associated (p&amp;lt;0.001) with Matsuda index in both cohorts. In the AAGMEx cohort, we identified cis-eQTLs (FDR&amp;lt;1%) for 786 Matsuda index-associated transcripts. Cis-eQTLs for 510 Matsuda index-associated genes were identified in both the AAGMEx and METSIM cohorts. These genes were enriched for mitochondrial dysfunction, phagosome maturation, and branched-chain amino acid degradation pathways. The enoyl-CoA hydratase domain-containing 3 (ECHDC3) was the top ranked Matsuda index-associated cis-eGene. ECHDC3 expression level was positively correlated with Matsuda index (r=0.47, p=5.3x10-15) and rs200943982 was the top ECHDC3 cis-eSNP (p=1.94x10-9) in AAGMEx. The shRNA-mediated silencing of ECHDC3 in SGBS adipocytes reduced insulin-stimulated Akt phosphorylation. RNA-seq analysis identified 691 differentially-expressed genes in ECHDC3 knockdown cells, which were enriched in γ-linolenate and cholesterol biosynthesis, LXR/RXR activation pathways, and known IR genes. In summary, variation-based genomic analysis with concurrent in vitro genetic silencing studies identified novel genetic regulatory mechanisms of IR. Disclosure N.K. Sharma: None. C.C. Key: None. M.E. Comeau: None. C.D. Langefeld: None. J.S. Parks: None. S.K. Das: None.